hmtnote 0.2.0

Human mitochondrial variants annotation using HmtVar.

HmtNote

Human mitochondrial variants annotation using HmtVar.

• Free software: MIT license

• Documentation: https://hmtnote.readthedocs.io.

Features

HmtNote is a bioinformatics tool that can be used to annotate human mitochondrial variants from a VCF, using data available on HmtVar.

Annotations are grouped into basic, cross-reference, variability and predictions, depending on the type of information they provide.

Basic

Basic information about the variant; they include:

• Locus: Locus to which the variant belongs

• AaChange: Aminoacidic change determined

• Pathogenicity: Pathogenicity predicted by HmtVar

• DiseaseScore: Disease score calculated by HmtVar

• HmtVar: HmtVar ID of the variant (can be used to view the related VariantCard on https://www.hmtvar.uniba.it/varCard/<HmtVarID>)

Cross-reference

Cross-reference information about the variant; they include:

• Clinvar: Clinvar ID of the variant

• dbSNP: dbSNP ID of the variant

• OMIM: OMIM ID of the variant

• MitomapAssociatedDiseases: Diseases associated to the variant according to Mitomap

• MitomapSomaticMutations: Diseases associated to the variant according to Mitomap Somatic Mutations

Variability

Variability and allele frequency data about the variant; they include:

• NtVarH: Nucleotide variability of the position in healthy individuals

• NtVarP: Nucleotide variability of the position in patient individuals

• AaVarH: Aminoacid variability of the position in healthy individuals

• AaVarP: Aminoacid variability of the position in patient individuals

• AlleleFreqH: Allele frequency of the variant in healthy individuals overall

• AlleleFreqP: Allele frequency of the variant in patient individuals overall

• AlleleFreqH_AF: Allele frequency of the variant in healthy individuals from Africa

• AlleleFreqP_AF: Allele frequency of the variant in patient individuals from Africa

• AlleleFreqH_AM: Allele frequency of the variant in healthy individuals from America

• AlleleFreqP_AM: Allele frequency of the variant in patient individuals from America

• AlleleFreqH_AS: Allele frequency of the variant in healthy individuals from Asia

• AlleleFreqP_AS: Allele frequency of the variant in patient individuals from Asia

• AlleleFreqH_EU: Allele frequency of the variant in healthy individuals from Europe

• AlleleFreqP_EU: Allele frequency of the variant in patient individuals from Europe

• AlleleFreqH_OC: Allele frequency of the variant in healthy individuals from Oceania

• AlleleFreqP_OC: Allele frequency of the variant in patient individuals from Oceania

Predictions

Pathogenicity prediction information of the variant from external resources; they include:

• MutPred_Prediction: Pathogenicity prediction offered by MutPred

• MutPred_Probability: Confidence of the pathogenicity prediction offered by MutPred

• Panther_Prediction: Pathogenicity prediction offered by Panther

• Panther_Probability: Confidence of the pathogenicity prediction offered by Panther

• PhDSNP_Prediction: Pathogenicity prediction offered by PhD SNP

• PhDSNP_Probability: Confidence of the pathogenicity prediction offered by PhD SNP

• SNPsGO_Prediction: Pathogenicity prediction offered by SNPs & GO

• SNPsGO_Probability: Confidence of the pathogenicity prediction offered by SNPs & GO

• Polyphen2HumDiv_Prediction: Pathogenicity prediction offered by Polyphen2 HumDiv

• Polyphen2HumDiv_Probability: Confidence of the pathogenicity prediction offered by Polyphen2 HumDiv

• Polyphen2HumVar_Prediction: Pathogenicity prediction offered by Polyphen2 HumVar

• Polyphen2HumVar_Probability: Confidence of the pathogenicity prediction offered by Polyphen2 HumVar

Usage

Command Line Interface

HmtNote can be used as a command line tool, by simply providing the original VCF and the filename where the annotated VCF will be saved:

hmtnote input_vcf.vcf annotated_vcf.vcf

By default, HmtNote will annotate the VCF using all four groups of annotations (basic, cross-reference, variability and predictions). If desired, you can specify which kind of annotation you want, using respectively --basic, --crossref, --variab and --predict (or -b, -c, -v, -p):

hmtnote input_vcf.vcf annotated_basic_vcf.vcf --basic
hmtnote input_vcf.vcf annotated_crossreferences_vcf.vcf --crossref
hmtnote input_vcf.vcf annotated_variability_vcf.vcf --variability
hmtnote input_vcf.vcf annotated_predictions_vcf.vcf --predict

Python Module

HmtNote can also be imported in a Python script and its function annotate_vcf() can be used to annotated a given VCF:

from hmtnote import annotate_vcf
annotate_vcf("input_vcf.vcf", "annotated_vcf.vcf")

By default, annotate_vcf() will annotate the VCF using all four groups of annotations (basic, cross-reference, variability and predictions). If desired, you can specify which kind of annotation you want, using respectively the basic=True, crossref=True, variab=True, predict=True arguments:

annotate_vcf("input_vcf.vcf", "annotated_basic_vcf.vcf", basic=True)
annotate_vcf("input_vcf.vcf", "annotated_crossreferences_vcf.vcf", crossref=True)
annotate_vcf("input_vcf.vcf", "annotated_variability_vcf.vcf", variab=True)
annotate_vcf("input_vcf.vcf", "annotated_predictions_vcf.vcf", predict=True)

Installation

PLEASE NOTE: HmtNote only supports Python 3!

The preferred installation method for HmtNote is using pip in a conda environment:

$ conda install requests
$ conda install -c bioconda cyvcf2
$ pip install hmtnote

If you have issues, please refer to the Installation section of the Documentation.

Credits

This package was created with Cookiecutter and the cc-pypackage project template.

History

0.1.0 (2019-03-03)

• First release on PyPI.

0.1.1 (2019-03-04)

• Clean installation requirements for conda;

• Update documentation.

0.1.2 (2019-03-15)

• Classes and methods are protected where needed;

• Code style is clean.

0.1.3 (2019-03-17)

• Fix issue with –predict annotation, which didn’t retrieve the correct field from HmtVar.

0.1.4 (2019-03-19)

• Fix issue that prevented importing annotate_vcf() into Python scripts.

0.1.5 (2019-03-20)

• Add HmtVar ID of the variant in basic and full annotation;

• Change Disease Score annotation to DiseaseScore.

0.2.0 (WIP)

• Add warnings to hmtnote command to be compliant with future versions;

• Check internet connection before trying to annotate variants.

X.X.X (WIP)

• Add options to download the required databases locally;

• Use local databases to annotate variants (instead of calling HmtVar’s API);

• Fallback to using local databases when web connection is not available?